Human papillomavirus (HPV) infection of the cervix can result in squamous intraepithelial neoplasia that can progress through increasing less differentiated stages that can give rise to squamous cell cancer of the cervix. The vast majority of cervix cancers are associated with high risk HPV types. Cancer is thought to result from inactivation of p53 by HPV E6 and pRB by HPV E7 proteins. p53 is the guardian of the genome and protects against DNA damage and pRB is a major G1 check point in the cell cycle. Abrogation of these activities by high risk HPV oncoproteins can result in the accumulation of mutations and eventually cancer. Early events in the progression of squamous intraepithelial lesions (SIL) to cancer are not well understood. However, it has been postulated that a change in the physical state of the viral genome (episomal to integrated form) may precipitate cancer development. Testing this hypothesis in a prospective manner cannot be done. However, the response of high grade premalignant SIL to topical chemotherapeutic agents or placebo may provide insights into the relationship between state of the viral genome and clinical response. Approximately 150 patients with high grade SIL were randomized to placebo or topical all trans retinoic acid (atRA). The subjects were biopsied at baseline and week 12 (end of study) to determine clinical disease. Subjects treated with topical atRA for four days were significantly more likely to revert to normal or non-treatable disease state than subjects getting placebo (p=0.05). We hypothesize that SIL in a high proportion of patients that failed to respond to atRA contain transcripts derived from integrated HPV. These transcripts are more stable than those derived from episomal virus DNA and the level of viral oneoproteins is higher in cells with integrated sequences. atRA may not be able to decrease the levels of oncoproteins sufficiently low to induce lesion resolution in those lesions containing integrated HPV DNA. We will determine the ratios of 5' (E7) and 3' (E5) sequences in reversed transcribed RNA obtained from formalin-fixed biopsies taken at baseline and week 12. If the ratio of E7:E5 approximates 1 then sequences are episomal; E7:E5 >1 then E5 sequences are underrepresented due to integration of virus DNA. Demonstration that atRA-resistant SIL contain transcripts derived from integrated HPV DNA would provide a powerful biomarker to identify those women who would likely fail nonablative therapy and who would be at increased risk of progression to cervical cancer.